Pokemon AquaRed
by aloasa
Summary: The champion in the Kanto region is consider the most powerful and benevolent person in the land, but, what if Red wasn't in the light of Justice all of his life, what if he work for one of the most notorious criminal teams ever? What if something involving it's destruction made him go into the light? Rated M (Game based with Anime and Manga elements)


The world of Pokémon, fill with the most incredible of creatures with imaginable powers, everyday both Pokémon and humans live in harmony, bond together, travel alongside each other and fight each other in the events known as Poke-Battles. Pokémon that train Pokémon in order to enter these competitions are called Pokémon trainers, they train their Pokémon in order to win money, gain fame, protection, any reason you can imagine.

Most of these trainers wish to one day be able to challenge the 8 Gym Leaders in order to access victory road, defeat the gauntlet called Elite 4 and battle the Champion in order to become the new Champion, in the region of Kanto the champion is arguably the most recognize champion in all the world, his name is a mystery and he is only refer as Red.

Red is the most powerful of the champions, defeating the other champions in friendly competitions, showing off his authority throughout all the land, no one dares to question him or hurt him in fear of his wrath, although in reality he one of the most kind people you could meet as long as you don't dare to treat Pokémon incorrectly.

But not all is bright in this world, as there are criminal groups working in the shadows, creating chaos and havoc all around, only a selected few have manage to make a name for themselves before being crush, one of these teams was Team Aqua. This is where this story begins, in the deeps of this evil organization where the one known as the Pokémon Master used to work.

* * *

Team Aqua was known to be one of the two most dangerous group of criminals in the land of Hoenn, their goal was to flood the world with the awakening of the mythical Pokémon Kyogre, this wasn't a ordinary goal as this could easily mean the destruction of homes, landscape and even extinction of Pokémon species. These people weren't to be taken lightly.

"Intruder alert! Intruder alert! An intruder has been spotted in the base! All personal is requested to capture the intruder!" A voice in the megaphone that where all around the base reported to the grunts. An intruder had been seen in the secret base and could possibly mean trouble for them if he got out. He had to be stop immediately or risk being discover.

"There he is, surround him!" a grunt located the unwanted visitor and soon after a whole battalion surrounded the poor soul, he wasn't putting any resistance at all, like if he wanted to be capture.

"So, what have we here?" Said a woman that approached the intruder, she was wearing a black top with an open blue jacket that left her belly area unclothed, a pair of blue and white pants with red shoes, a pair of blue gloves and a blue bandanna with the Aqua symbol on it that she tied on her long red hair. "A Magma grunt actually had the guts to enter our secret base, and with no backup." She said getting closer to her, grabbing one of her pokeballs.

Team Magma was the polar opposite, their goal was the increase of the landscape by summoning Groundon. Although it wasn't as ridiculous as increasing the water levels it was a worst fate considering the extinction of many types of water Pokémon and finally the water problems that would become of this process. These two organizations hated each other, so they fight over supremacy in the shadows and in the eyes of people they would create propaganda of all sorts in order to antagonized the other team and have more followers themselves.

"So tell me, why shouldn't I simply deal with you right now in front of all my subordinates" She threaten the intruder, but he didn't move nor sweat, not even flinch, he only smirk at her. "You know, your cute when you do that, BUT, you really are an idiot sometimes" He responded to her, earning a blush and a scold at the same time from the woman.

"Ok, that's it, you asked for it" She said, releasing her Pokémon, a gray canine known as Mightyena, he left a small growl but he sniff a little, recognizing the hooded man and pounce on him, making him fall on his back, and the canine began licking his face, confusion was present on every single grunt on the circle until the owner of the Pokémon just remember something.

"Wait a minute, Red?" She surprisingly asked the hooded man, he smirk as he took off his Magma grunt clothes. "About time" he coldly said to her "I was beginning to wonder how much time would I have to act like this, even your Mightyena saw who I was before you, and you call yourself an Admin?" He ranted to her, completely angry at the events. "Sorry guys, false alarm, it was just Red" She told the grunts and they all begrudgingly leaved, one of them even cussing them off as he left for wasting his time.

"Oh yeah? You try and return here after escaping a burning Magma base, fighting off grunt after grunt AND getting here unnoticed until your incompetence negated you from seeing who I am and treating me as a intruder" Red furiously remark is actions in order to get the grunt out of there, he wasn't in the mood for these kind of grunts.

Shelly was lost at words for a bit, only reacting the moment Red ended his word battle with the grunt, and she was angry at him for pulling this kind of stunt, again. She receive Red with a smack to the head. "Ouch, what was THAT for, Shelly?" He rubbed his head because of the pain. "Well let me get started, first you keep me in the shadows of your infiltration, I had to hear it from a grunt!" She started her rant against him for his actions, to which he began to walk backwards in fear.

"Second, you leave all ways of being able to communicate with you!" She had him pin against a wall at this point. "Third, you don't even send your reports and that's the only way I can know that you're safe" "Wow, you actually care for me, that's new" He pointed out between her sentence, earning a second smack to the back of his head "Ouch, stop that" he whine from the pain, but she ignore that "And finally you dare come here without saying a word, and scramble the whole base! I could of hurt you enough for you not to be able to be an Admin!" She ended her rant completely exhausted from all the yelling at him, he only had a questionable look and said "Is that your way to say that you miss me?"

"Ouch, hey, cut it out, I may become dumb like you, OUCH!" He continue to receive smack in the head each time he spoke, making her anger less and less each time, the hits also got weaker. "Better?" He ask Shelly, rubbing his head and feeling the bump he now has. "Yeah, I'm feeling better" She said truthfully to him. "Good, sorry if I couldn't tell you, it was a top secret mission and I couldn't tell anyone about it, not even you, I'm so sorry Shelly" He apologized to her, with his head looking to the ground and a serious look on his face, not something you would see everyday, she just pull him into a tight hug.

"Yeah, I did miss you, next time tell me, you know you can trust me" She said to him, completely relief he return the hug and maintain it for maybe a minute before letting go. "Come on, we need to brief you of our activity with the boss, and you have to explain about your mission." She explain to him and both of them began to walk towards the Leader's room.

"So... what exactly happen with Courtney?" She asked randomly, cracking her knuckles, waiting for his response. "Umm...about that" He said, gulping.

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**And here is the first part of the prologue of Pokémon Aqua Red, I hope you enjoy this project, the idea came from a challenge that I had in a forum called Ever Grande City (shameless advertisement FTW! XD) that require you to choose a team, either Aqua or Magma, and use Pokémon according to the typing, the only other typings you could use is Dark, Poison and of course Mightyena or any of the Rattata clones, and complete any main Pokémon game. I choose to play Firered and it's been a fun challenge, and then the idea for the fic came to me, what if Red wasn't that innocent? You'll see what happens as it goes out in the following chapters, now...I would like to request some sort of beta reader or something, I really need help with the english language D: **

**As of stuff in this fic... It will be either a harem of sorts or simply RedxShelly with RedxCourtney and Redx? hints, I like the harem idea better because of how I could play with Shelly's character her as I write along. So, this is all for now...oh wait, I'm forgetting something... oh yeah, I'll try and add lemons in the future, keyword try.**

**Finally, I'm putting my south park fanfic in hiatus because writer's block, I can't write anything for it D:**

**Anyway, that's it for now, so keep in tune with me, next week on the same page, for more Pokémon Aqua Red.**

**Aloasa, signing off.**

**Pokémon and it's characters are own by Game Freak.**


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